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- PDB-4jmi: Sec7 domain of ARNO, an exchange factor, at 1.5 Angstrom resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jmi | ||||||
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Title | Sec7 domain of ARNO, an exchange factor, at 1.5 Angstrom resolution | ||||||
![]() | Cytohesin-2 | ||||||
![]() | SIGNALING PROTEIN / Nucleotide Exchange Factors / Arf1 | ||||||
Function / homology | ![]() Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / guanyl-nucleotide exchange factor activity / adherens junction / endocytosis / growth cone / actin cytoskeleton organization / Golgi membrane ...Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / guanyl-nucleotide exchange factor activity / adherens junction / endocytosis / growth cone / actin cytoskeleton organization / Golgi membrane / lipid binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoh, F. / Rouhana, J. | ||||||
![]() | ![]() Title: Fragment-based identification of a locus in the Sec7 domain of Arno for the design of protein-protein interaction inhibitors Authors: Rouhana, J. / Hoh, F. / Estaran, S. / Henriquet, C. / Boublik, Y. / Kerkour, A. / Trouillard, R. / Martinez, J. / Pugniere, M. / Padilla, A. / Chavanieu, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.7 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.2 KB | Display | ![]() |
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Full document | ![]() | 414.4 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jmoC ![]() 4jwlC ![]() 4jxhC ![]() 4l5mC ![]() 1pbvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23029.312 Da / Num. of mol.: 1 / Fragment: Sec7 domain, UNP residues 56-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M MgSO4, Peg 5000 MME 18%, 0.1M Mes pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→44.77 Å / Num. all: 38574 / Num. obs: 38574 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.5→1.58 Å / Rmerge(I) obs: 0.342 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PBV Resolution: 1.5→44.77 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.661 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.079 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→44.77 Å
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Refine LS restraints |
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